From owner-chemistry@ccl.net Wed May 11 00:31:01 2011 From: "Arvydas.Tamulis|tfai.vu.lt" To: CCL Subject: CCL: micelle structure (PDB) files Message-Id: <-44613-110511002706-31052-3s7dA6s3iGvgVW68U3wihw*_*server.ccl.net> X-Original-From: Arvydas.Tamulis,tfai.vu.lt Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Wed, 11 May 2011 07:26:46 +0300 MIME-Version: 1.0 Sent to CCL by: Arvydas.Tamulis{}tfai.vu.lt Dear Andreas, MD simulations give wrong results of micelle structure and even semiempirical QM methods are not sufficient. Please take a look to our DFT non local gradient investigations: A. Tamulis, M. Grigalavicius, „The Emergence and Evolution of Life in a “Fatty Acid World” Based on Quantum Mechanics”, Origins of Life and Evolution of Biospheres, 2011) vol. 41, pages 51-71. Electronical version of this article with moving micelles available at http://www.springerlink.com/content/7122n16869843314/fulltext.html Would you please to accept my proposal to cooperate in further investigations of micelles in the case if you have large computing possibilities. With best regards, Arvydas http://www.itpa.lt/~tamulis/ "Andreas Klamt klamt|-|cosmologic.de" rašė: > > Sent to CCL by: Andreas Klamt [klamt^^^cosmologic.de] > Dear CCLers, > > this time I like to post a question instead of commenting on other > peoples questions: > > Does anyone know a larger reservoir of micelle structure data (most > like stored in PDB format)? We would be interested in collecting > such structures, either based on experimental data or on MD > simulations. Maybe we could host a library of such files or a > library of links to such files on our web site. > > In the moment we are especially interested in SLES micelles. > > Thanks in advance > > Andreas Klamthttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Wed May 11 01:50:01 2011 From: "Andreas Klamt klamt**cosmologic.de" To: CCL Subject: CCL: micelle structure (PDB) files Message-Id: <-44614-110511014311-28733-643ytHOW4tC3a6kk8RD7ag(a)server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 11 May 2011 07:43:01 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt[#]cosmologic.de] Dear Arvydas, thank you very much for your reply, but from your paper I cannot really see how you can conclude that MD results on micelles and bio-membranes should be generally wrong. To our experience such simulations give a reasonable picture of the composition, i.e. of probability to find certain parts of surfactants and solvent molecules in the layers of the micelle, and that is what we need to know in order to calculate the free energy of solutes in such micelles with the COSMOmic tool. We do not see major diferences in the COSMOmic results depending on which specific MD results we are using as input for the micelle composition. It seems that they are rather comverged in that regard. Andreas Am 11.05.2011 06:26, schrieb Arvydas.Tamulis|tfai.vu.lt: > > Sent to CCL by: Arvydas.Tamulis{}tfai.vu.lt > Dear Andreas, > > MD simulations give wrong results of micelle structure and even > semiempirical QM methods are not sufficient. > Please take a look to our DFT non local gradient investigations: > A. Tamulis, M. Grigalavicius, „The Emergence and Evolution of Life in > a “Fatty Acid World” Based on Quantum Mechanics”, Origins of Life and > Evolution of Biospheres, 2011) vol. 41, pages 51-71. Electronical > version of this article with moving micelles available at > http://www.springerlink.com/content/7122n16869843314/fulltext.html > > Would you please to accept my proposal to cooperate in further > investigations of micelles in the case if you have large computing > possibilities. > > With best regards, > Arvydas > http://www.itpa.lt/~tamulis/ > > "Andreas Klamt klamt|-|cosmologic.de" rašė: > >> >> Sent to CCL by: Andreas Klamt [klamt^^^cosmologic.de] >> Dear CCLers, >> >> this time I like to post a question instead of commenting on other >> peoples questions: >> >> Does anyone know a larger reservoir of micelle structure data (most >> like stored in PDB format)? We would be interested in collecting such >> structures, either based on experimental data or on MD simulations. >> Maybe we could host a library of such files or a library of links to >> such files on our web site. >> >> In the moment we are especially interested in SLES micelles. >> >> Thanks in advance >> >> Andreas Klamthttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >> http://server.ccl.net/chemistry/announcements/conferences/http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- PD. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH& Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt..cosmologic.de web www.cosmologic.de HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Wed May 11 02:24:01 2011 From: "Sebastian Kozuch kozuchs-x-yahoo.com" To: CCL Subject: CCL:G: van-der-Waals-complex vs. weak forces Message-Id: <-44615-110511014141-27480-HhwaYd9ZzIZ7kyP2+1oKZg*_*server.ccl.net> X-Original-From: Sebastian Kozuch Content-Type: multipart/alternative; boundary="0-298607376-1305092491=:81580" Date: Tue, 10 May 2011 22:41:31 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [kozuchs%a%yahoo.com] --0-298607376-1305092491=:81580 Content-Type: text/plain; charset=us-ascii Take a look at the NCIPlot program. It analyses the different non-covalent interactions, and using VMD you can have nice plots of them. I'm not sure, but I think that although b97d will give you proper geometries and energies, it will not be appropriate for NCIPlot, since the dispersion correction does not act into the electronic density, thus not being taken into account into the program. I may use for single point energies a method that intrinsically includes dispersion forces (M06-2X maybe), but that has to be tested. Best, xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ..........Sebastian Kozuch........... xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ....Weizmann Institute of Science.... ...........Rehovot, Israel........... .. sebastian.kozuch!A!weizmann.ac.il .. http://yfaat.ch.huji.ac.il/kozuch.htm xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ________________________________ > From: Guntram Schmidt guntram.schmidt]=[chemie.uni-halle.de To: "Kozuch, Sebastian " Sent: Tue, May 10, 2011 10:45:00 PM Subject: CCL:G: van-der-Waals-complex vs. weak forces Sent to CCL by: "Guntram Schmidt" [guntram.schmidt(-)chemie.uni-halle.de] Hello together! I want to exam some (mainly organic) crystal structures, which seem to be mainly held together by weak forces like Phenyl-H---O hydrogen bonds, Phenly-H---Phenyl hydrogen bonds or Pi-Pi-stacking. I cut out the corresponding dimers of the crystal structure and subjected them to geometry optimisation, using gaussian 09 with the input line #T opt freq b97d/6-31g(d,p)/auto=all which works quite well, resulting in minima for expected bonding, but striding away molecules for dimers which are not supposed to interact in a "bonding" way. Now having some optimized structures, is there anything to do to prove the nature of the "bonding"? How can I distinguish the "van-der-Waals complex" from a dispersion interaction or some kind of hydrogen bonding? Thanks a lot for suggestions on how to treat this problem, Guntramhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-298607376-1305092491=:81580 Content-Type: text/html; charset=us-ascii
Take a look at the NCIPlot program. It analyses the different non-covalent interactions, and using VMD you can have nice plots of them.
I'm not sure, but I think that although b97d will give you proper geometries and energies, it will not be appropriate for NCIPlot, since the dispersion correction does not act into the electronic density, thus not being taken into account into the program. I may use for single point energies a method that intrinsically includes dispersion forces (M06-2X maybe), but that has to be tested.

Best,
 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
....Weizmann Institute of Science....
...........Rehovot, Israel...........
.. sebastian.kozuch!A!weizmann.ac.il ..
http://yfaat.ch.huji.ac.il/kozuch.htm
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx


From: Guntram Schmidt guntram.schmidt]=[chemie.uni-halle.de <owner-chemistry!A!ccl.net>
To: "Kozuch, Sebastian " <kozuchs!A!yahoo.com>
Sent: Tue, May 10, 2011 10:45:00 PM
Subject: CCL:G: van-der-Waals-complex vs. weak forces


Sent to CCL by: "Guntram  Schmidt" [guntram.schmidt(-)chemie.uni-halle.de]
Hello together!

I want to exam some (mainly organic) crystal structures, which seem to be mainly held together by weak forces like Phenyl-H---O hydrogen bonds, Phenly-H---Phenyl hydrogen bonds or Pi-Pi-stacking.

I cut out the corresponding dimers of the crystal structure and subjected them to geometry optimisation, using gaussian 09 with the input line

#T opt freq b97d/6-31g(d,p)/auto=all

which works quite well, resulting in minima for expected bonding, but striding away molecules for dimers which are not supposed to interact in a "bonding" way.

Now having some optimized structures, is there anything to do to prove the nature of the "bonding"?
How can I distinguish the "van-der-Waals complex" from a dispersion interaction or some kind of hydrogen bonding?


Thanks a lot for suggestions on how to treat this problem,
Guntram



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--0-298607376-1305092491=:81580-- From owner-chemistry@ccl.net Wed May 11 14:40:00 2011 From: "Shahar Keinan skeinan*gmail.com" To: CCL Subject: CCL:G: van-der-Waals-complex vs. weak forces Message-Id: <-44616-110511093804-3758-uk/sOuoFkSFk7YONhBJC7w|,|server.ccl.net> X-Original-From: Shahar Keinan Content-Type: multipart/alternative; boundary=000e0cd3282eb5db9804a3002dec Date: Wed, 11 May 2011 09:37:48 -0400 MIME-Version: 1.0 Sent to CCL by: Shahar Keinan [skeinan!=!gmail.com] --000e0cd3282eb5db9804a3002dec Content-Type: text/plain; charset=ISO-8859-1 I do think the NCIplot is an excellent option. Let me just state here, that even if the functional that you are using don't include dispersion corrections, the underlaying density does have the correct dispersion, and thus NCIplot will be able to display vDW and Hydrogen bonds. We have several such examples in the supporting information of the manuscript: http://pubs.acs.org/doi/suppl/10.1021/ja100936w Here is the website for more information about the method and how to download the code: http://www.chem.duke.edu/~yang/Software/softwareNCI.html I am one of the developers, and this email is part of our shameless promotion division :) Anyway, if you have problems/questions, don't hesitate to contact me, Shahar On Wed, May 11, 2011 at 1:41 AM, Sebastian Kozuch kozuchs-x-yahoo.com < owner-chemistry ~ ccl.net> wrote: > Take a look at the NCIPlot program. It analyses the different non-covalent > interactions, and using VMD you can have nice plots of them. > I'm not sure, but I think that although b97d will give you proper > geometries and > energies, it will not be appropriate for NCIPlot, since the dispersion > correction does not act into the electronic density, thus not being taken > into > account into the program. I may use for single point energies a method that > intrinsically includes dispersion forces (M06-2X maybe), but that has to be > tested. > > Best, > > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > ..........Sebastian Kozuch........... > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > ....Weizmann Institute of Science.... > ...........Rehovot, Israel........... > .. sebastian.kozuch^weizmann.ac.il .. > http://yfaat.ch.huji.ac.il/kozuch.htm > xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx > > > > > ________________________________ > > From: Guntram Schmidt guntram.schmidt]=[chemie.uni-halle.de > > To: "Kozuch, Sebastian " > Sent: Tue, May 10, 2011 10:45:00 PM > Subject: CCL:G: van-der-Waals-complex vs. weak forces > > > Sent to CCL by: "Guntram Schmidt" [guntram.schmidt(-)chemie.uni-halle.de] > Hello together! > > I want to exam some (mainly organic) crystal structures, which seem to be > mainly > held together by weak forces like Phenyl-H---O hydrogen bonds, > Phenly-H---Phenyl > hydrogen bonds or Pi-Pi-stacking. > > I cut out the corresponding dimers of the crystal structure and subjected > them > to geometry optimisation, using gaussian 09 with the input line > > #T opt freq b97d/6-31g(d,p)/auto=all > > which works quite well, resulting in minima for expected bonding, but > striding > away molecules for dimers which are not supposed to interact in a "bonding" > way. > > Now having some optimized structures, is there anything to do to prove the > nature of the "bonding"? > How can I distinguish the "van-der-Waals complex" from a dispersion > interaction > or some kind of hydrogen bonding? > > > Thanks a lot for suggestions on how to treat this problem, > Guntramhttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-298607376-1305092491=:81580 > Content-Type: text/html; charset=us-ascii > >
style="font-family:arial,helvetica,sans-serif;font-size:10pt">Take a look at > the NCIPlot program. It analyses the different non-covalent interactions, > and using VMD you can have nice plots of them.
I'm not sure, but I think > that although b97d will give you proper geometries and energies, it will not > be appropriate for NCIPlot, since the dispersion correction does not act > into the electronic density, thus not being taken into account into the > program. I may use for single point energies a method that intrinsically > includes dispersion forces (M06-2X maybe), but that has to be > tested.

Best,
 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
style="font-family:courier, monaco, monospace, sans-serif;"> style="font-family:courier, monaco, monospace, > sans-serif;">..........Sebastian Kozuch...........
style="font-family:courier, monaco, monospace, sans-serif;"> style="font-family:courier, monaco, monospace, > sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
style="font-family:courier, monaco, monospace, sans-serif;"> style="font-family:courier, monaco, monospace, sans-serif;">....Weizmann > Institute of Science....
...........Rehovot, Israel...........
style="font-family:courier, monaco, monospace, sans-serif;"> style="font-family:courier, monaco, monospace, sans-serif;">.. > sebastian.kozuch^weizmann.ac.il ..
href="http://yfaat.ch.huji.ac.il/kozuch.htm"> style="font-family:courier, monaco, monospace, sans-serif;"> > http://yfaat.ch.huji.ac.il/kozuch.htm
style="font-family:courier, monaco, monospace, sans-serif;"> style="font-family:courier, monaco, monospace, > sans-serif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

style="font-family:arial, helvetica, sans-serif;font-size:10pt">
style="font-family:arial, helvetica, sans-serif;font-size:10pt"> face="Tahoma" size="2">
From: Guntram Schmidt guntram.schmidt]=[ > chemie.uni-halle.de <owner-chemistry^ccl.net>
style="font-weight: bold;">To: "Kozuch, Sebastian " <kozuchs^ > yahoo.com>
Sent: Tue, > May 10, 2011 10:45:00 PM
Subject: CCL:G: van-der-Waals-complex vs. weak > forces


Sent to CCL by: "Guntram  Schmidt" > [guntram.schmidt(-)chemie.uni-halle.de]
Hello together!

I want > to exam some (mainly organic) crystal structures, which seem to be mainly > held together by weak forces like Phenyl-H---O hydrogen bonds, > Phenly-H---Phenyl hydrogen bonds or Pi-Pi-stacking.

I cut out the > corresponding dimers of the crystal structure and subjected them to geometry > optimisation, using gaussian 09 with the input line

#T opt freq > b97d/6-31g(d,p)/auto=all

which works quite well, resulting in minima > for expected bonding, but striding away molecules for dimers which are not > supposed to interact in a "bonding" way.

Now having some optimized > structures, is there anything to do to prove the nature of the > "bonding"?
How can I distinguish the "van-der-Waals complex" from a > dispersion interaction or some kind of hydrogen bonding?


Thanks a > lot for suggestions on how to treat > this problem,
Guntram



E-mail to > subscribers: CHEMISTRY^ccl.net or use:
     

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-- ------------------------------------------------------ Shahar Keinan (919) 357 5319 --000e0cd3282eb5db9804a3002dec Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I do think the NCIplot is an excellent option.

Let me ju= st state=A0here, that even if the functional that you are using don't i= nclude=A0dispersion=A0corrections, the underlaying density does have the co= rrect dispersion, and thus NCIplot will be able to=A0display=A0vDW and Hydr= ogen bonds. We have several such examples in the supporting information of = the manuscript:

Here is the we= bsite for more information about the method and how to download the code:

<= div>I am one of the developers, and this email is part of our shameless pro= motion division :)

Anyway, if you have problems/questions, don't hesit= ate to contact me,
Shahar


On Wed, May 11, 2011 at 1:41 AM, Sebastian Kozuch kozuchs-x-yahoo.com <owner-chemistry ~ ccl.net> = wrote:
Take a look at the NCIPlot program. It anal= yses the different non-covalent
interactions, and using VMD you can have nice plots of them.
I'm not sure, but I think that although b97d will give you proper geome= tries and
energies, it will not be appropriate for NCIPlot, since the dispersion
correction does not act into the electronic density, thus not being taken i= nto
account into the program. I may use for single point energies a method that=
intrinsically includes dispersion forces (M06-2X maybe), but that has to be=
tested.

Best,

=A0xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
....Weizmann Institute of Science....
...........Rehovot, Israel...........
.. sebastian.kozuch^wei= zmann.ac.il ..
http://= yfaat.ch.huji.ac.il/kozuch.htm
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx




________________________________
> From: Guntram Schmidt guntram.schmidt]=3D[chemie.uni-halle.de
<owner-chemistry^ccl.net>
To: "Kozuch, Sebastian " <kozuchs^yahoo.com>
Sent: Tue, May 10, 2011 10:45:00 PM
Subject: CCL:G: van-der-Waals-complex vs. weak forces


Sent to CCL by: "Guntram =A0Schmidt" [guntram.schmidt(-)chemie.uni-halle.de]<= br> Hello together!

I want to exam some (mainly organic) crystal structures, which seem to be m= ainly
held together by weak forces like Phenyl-H---O hydrogen bonds, Phenly-H---P= henyl
hydrogen bonds or Pi-Pi-stacking.

I cut out the corresponding dimers of the crystal structure and subjected t= hem
to geometry optimisation, using gaussian 09 with the input line

#T opt freq b97d/6-31g(d,p)/auto=3Dall

which works quite well, resulting in minima for expected bonding, but strid= ing
away molecules for dimers which are not supposed to interact in a "bon= ding" way.

Now having some optimized structures, is there anything to do to prove the<= br> nature of the "bonding"?
How can I distinguish the "van-der-Waals complex" from a dispersi= on interaction
or some kind of hydrogen bonding?


Thanks a lot for suggestions on how to treat this problem,
Guntramhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehtt= p://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0= -298607376-1305092491=3D:81580
Content-Type: text/html; charset=3Dus-ascii

<html><head><style type=3D"text/css"><!-- DI= V {margin:0px;} --></style></head><body><div style= =3D"font-family:arial,helvetica,sans-serif;font-size:10pt">Tak= e a look at the NCIPlot program. It analyses the different non-covalent int= eractions, and using VMD you can have nice plots of them.<br>I'm = not sure, but I think that although b97d will give you proper geometries an= d energies, it will not be appropriate for NCIPlot, since the dispersion co= rrection does not act into the electronic density, thus not being taken int= o account into the program. I may use for single point energies a method th= at intrinsically includes dispersion forces (M06-2X maybe), but that has to= be tested.<br><br>Best,<br><div>&nbsp;</div= ><span style=3D"font-family:courier, monaco, monospace, sans-ser= if;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><br style= =3D"font-family:courier, monaco, monospace, sans-serif;"><s= pan style=3D"font-family:courier, monaco, monospace,
=A0sans-serif;">..........Sebastian Kozuch...........</span>&= lt;br style=3D"font-family:courier, monaco, monospace, sans-serif;&quo= t;><span style=3D"font-family:courier, monaco, monospace, sans-s= erif;">xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><br sty= le=3D"font-family:courier, monaco, monospace, sans-serif;"><= ;span style=3D"font-family:courier, monaco, monospace, sans-serif;&quo= t;>....Weizmann Institute of Science....</span><br style=3D&quo= t;font-family:courier, monaco, monospace, sans-serif;"><span sty= le=3D"font-family:courier, monaco, monospace, sans-serif;">...= ........</span><span style=3D"font-family:courier, monaco, mo= nospace, sans-serif;">Rehovot, Israel...........</span><br= style=3D"font-family:courier, monaco, monospace, sans-serif;">= ;<span style=3D"font-family:courier, monaco, monospace, sans-serif;= ">.. sebastian.kozuch^weizmann.ac.il ..</span><br style=3D"font-family:c= ourier, monaco, monospace, sans-serif;"><a rel=3D"nofollow&= quot; target=3D"_blank"
=A0href=3D"http://yfaat.ch.huji.ac.il/kozuch.htm"><span style= =3D"font-family:courier, monaco, monospace, sans-serif;">http://yfaat= .ch.huji.ac.il/kozuch.htm</span></a><br style=3D"fo= nt-family:courier, monaco, monospace, sans-serif;"><span style= =3D"font-family:courier, monaco, monospace, sans-serif;">xxxxx= xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</span><div><br></div&= gt;<div style=3D"font-family:arial, helvetica, sans-serif;font-size= :10pt"><br><div style=3D"font-family:arial, helvetica= , sans-serif;font-size:10pt"><font face=3D"Tahoma" siz= e=3D"2"><hr size=3D"1"><b><span style= =3D"font-weight: bold;">From:</span></b> Guntram S= chmidt guntram.schmidt]=3D[chemie.uni-halle.de &lt;owner-chemistry^ccl.net&gt;<br><b><span s= tyle=3D"font-weight: bold;">To:</span></b> "K= ozuch, Sebastian " &lt;kozuchs^yahoo.com&gt;<br><b><span style=3D"= font-weight: bold;">Sent:</span></b> Tue, May 10, 2011 = 10:45:00 PM<br><b><span style=3D"font-weight: bold;&quo= t;>Subject:</span></b> CCL:G: van-der-Waals-complex vs. weak=
=A0forces<br></font><br><br>Sent to CCL by: "G= untram&nbsp; Schmidt" [guntram.schmidt(-)chemie.uni-halle.de]<br>Hello tog= ether!<br><br>I want to exam some (mainly organic) crystal stru= ctures, which seem to be mainly held together by weak forces like Phenyl-H-= --O hydrogen bonds, Phenly-H---Phenyl hydrogen bonds or Pi-Pi-stacking.<= br><br>I cut out the corresponding dimers of the crystal structure= and subjected them to geometry optimisation, using gaussian 09 with the in= put line<br><br>#T opt freq b97d/6-31g(d,p)/auto=3Dall<br>= ;<br>which works quite well, resulting in minima for expected bonding= , but striding away molecules for dimers which are not supposed to interact= in a "bonding" way.<br><br>Now having some optimized= structures, is there anything to do to prove the nature of the "bondi= ng"?<br>How can I distinguish the "van-der-Waals complex&qu= ot; from a dispersion interaction or some kind of hydrogen bonding?<br&g= t;<br><br>Thanks a lot for suggestions on how to treat
=A0this problem,<br>Guntram<br><br><br><br<br= <br<br<br><br>E-mail to subscribers: <a ymailto=3D&quo= t;mailto:CHEMISTRY^ccl.net" href=3D"mailto:CHEMISTRY^cc= l.net">CHEMISTRY^c= cl.net</a> or use:<br>&nbsp; &nbsp; &nbsp; <= a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_message"= target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_= message</a><br><br>E-mail to administrators: <a ym= ailto=3D"mailto:CHEMISTRY-REQUEST= ^ccl.net" href=3D= "mailto:CHEMISTRY-REQUEST^ccl.net">CHEMISTRY-RE= QUEST^ccl.net</a> or= use<br>&nbsp; &nbsp; &nbsp; <a href=3D"http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message" target=3D"_blank= ">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>&= lt;br><br<br>&nbsp; &nbsp; &nbsp; <a
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Sh= ahar Keinan
(919) 357 5319
--000e0cd3282eb5db9804a3002dec-- From owner-chemistry@ccl.net Wed May 11 20:51:01 2011 From: "arslan ali arslanali1986{:}gmail.com" To: CCL Subject: CCL: which basis set Message-Id: <-44617-110510100622-31165-B/UIWzXOEFksnrWAQDCWgw-x-server.ccl.net> X-Original-From: arslan ali Content-Type: multipart/alternative; boundary=0016e6dcd27d75d3a404a2ec757b Date: Tue, 10 May 2011 07:06:13 -0700 MIME-Version: 1.0 Sent to CCL by: arslan ali [arslanali1986]-[gmail.com] --0016e6dcd27d75d3a404a2ec757b Content-Type: text/plain; charset=ISO-8859-1 hi, can anybody please tell me, which basis set in DFT will be more appropriate for geometry optimization of molecules of aprox 500 amu containing CHNO elements only?? thanks in advance Arslan --0016e6dcd27d75d3a404a2ec757b Content-Type: text/html; charset=ISO-8859-1 hi,

can anybody please tell me, which basis set in DFT will be more appropriate for geometry optimization of molecules of aprox 500 amu containing CHNO elements only??

thanks in advance

Arslan
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